library(readxl)
library(here)
library(bayclumpr)
library(DT)Bayesian regressions - Foram paper
Load libraries
Below, I provide the analyses for 4 calibration datasets and 2 reconstruction datasets.
Test 1: All benthics Test 2: Infaunal + epifaunal (=all benthics-MB) Test 3: infaunal Test 4: epifaunal
Reconstruction A (1): Meckler Reconstruction B (2): EOT
Test 1
Calibration
Table1 <- read_excel(here("data", "Test 1.xlsx"))
Table1$Material <- rep(1, nrow(Table1))
colnames(Table1)[c(5, 6, 2, 3, 8)] <- c("D47", "D47error", "Temperature", "TempError", "Ion")
# Check basic regression model
lm(Table1$D47 ~ Table1$Temperature)
Call:
lm(formula = Table1$D47 ~ Table1$Temperature)
Coefficients:
(Intercept) Table1$Temperature
0.2981 0.0277 # Fit Bayesian regression
ionmodel <- cal.ion.bayesian(calibrationData = Table1,
IonError = Table1$`Ion error`[1])Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX13.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
In file included from <built-in>:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
#include <cmath>
^~~~~~~
1 error generated.
make: *** [foo.o] Error 1
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN
2SAMPLING).
FOR MODEL 'anon_model' NOW (CHAIN 1).
Chain 2:
Chain 2: Gradient evaluation took 0.000111 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.11 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 1:
Chain 1: Gradient evaluation took 0.000216 seconds
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Chain 1:
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Chain 1: 14.697 seconds (Total)
Chain 1: parameters <- data.frame(rstan::summary(ionmodel[[1]])$summary)
DT::datatable(
parameters,
extensions = c('Buttons', 'Scroller'),
options = list(
dom = 'Bfrtip',
buttons = list(
list(
extend = 'collection',
buttons = c('csv', 'excel', 'pdf'),
text = 'Download'
)
)
)
)Reconstruction 1
ionRec <- read_excel(here("data", "Test 1.xlsx"), sheet = 2)
colnames(ionRec)[2:5] <- c("D47", "D47error", "Ion", "Ionerror")
PredsBay <- rec.ion.bayesian(calModel = ionmodel[[1]],
recData = ionRec,
iter = 1000,
postcalsamples = 100, MC = FALSE)Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX13.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
In file included from <built-in>:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
#include <cmath>
^~~~~~~
1 error generated.
make: *** [foo.o] Error 1
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.001056 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 10.56 seconds.
Chain 1: Adjust your expectations accordingly!
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Chain 1: 19.755 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000514 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 5.14 seconds.
Chain 2: Adjust your expectations accordingly!
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Chain 2:
Chain 2: Elapsed Time: 10.366 seconds (Warm-up)
Chain 2: 9.02 seconds (Sampling)
Chain 2: 19.386 seconds (Total)
Chain 2: DT::datatable(
PredsBay,
extensions = c('Buttons', 'Scroller'),
options = list(
dom = 'Bfrtip',
buttons = list(
list(
extend = 'collection',
buttons = c('csv', 'excel', 'pdf'),
text = 'Download'
)
)
)
)Reconstruction 2
ionRec <- read_excel(here("data", "Test 1.xlsx"), sheet = 3)
colnames(ionRec)[2:5] <- c("D47", "D47error", "Ion", "Ionerror")
ionRec <- na.omit(ionRec)
PredsBay <- rec.ion.bayesian(calModel = ionmodel[[1]],
recData = ionRec,
iter = 1000,
postcalsamples = 100, MC = FALSE)Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX13.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
In file included from <built-in>:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
#include <cmath>
^~~~~~~
1 error generated.
make: *** [foo.o] Error 1
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000618 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 6.18 seconds.
Chain 1: Adjust your expectations accordingly!
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Chain 1:
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000311 seconds
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Chain 2: Adjust your expectations accordingly!
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Chain 2:
Chain 2: Elapsed Time: 10.359 seconds (Warm-up)
Chain 2: 7.269 seconds (Sampling)
Chain 2: 17.628 seconds (Total)
Chain 2: DT::datatable(
PredsBay,
extensions = c('Buttons', 'Scroller'),
options = list(
dom = 'Bfrtip',
buttons = list(
list(
extend = 'collection',
buttons = c('csv', 'excel', 'pdf'),
text = 'Download'
)
)
)
)Test 2
Calibration
Table1 <- read_excel(here("data", "Test 2.xlsx"))
Table1$Material <- rep(1, nrow(Table1))
colnames(Table1)[c(5, 6, 2, 3, 8)] <- c("D47", "D47error", "Temperature", "TempError", "Ion")
# Check basic regression model
lm(Table1$D47 ~ Table1$Temperature)
Call:
lm(formula = Table1$D47 ~ Table1$Temperature)
Coefficients:
(Intercept) Table1$Temperature
0.2137 0.0343 # Fit Bayesian regression
ionmodel <- cal.ion.bayesian(calibrationData = Table1,
IonError = Table1$`Ion error`[1])Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX13.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
In file included from <built-in>:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
#include <cmath>
^~~~~~~
1 error generated.
make: *** [foo.o] Error 1
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 1).
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 2).
Chain 1:
Chain 1: Gradient evaluation took 7.4e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.74 seconds.
Chain 1: Adjust your expectations accordingly!
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Chain 2: Gradient evaluation took 9.6e-05 seconds
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Chain 1: 11.81 seconds (Total)
Chain 1: parameters <- data.frame(rstan::summary(ionmodel[[1]])$summary)
parameters mean se_mean sd X2.5. X25.
alpha 1.492774e-01 8.466368e-04 4.988167e-02 5.095852e-02 1.161086e-01
beta 3.874111e-02 6.352834e-05 3.782881e-03 3.118677e-02 3.625712e-02
gamma 1.790384e-04 1.354123e-06 7.353781e-05 3.611365e-05 1.304195e-04
sigma 1.177953e-02 2.428894e-05 1.484352e-03 9.331865e-03 1.074965e-02
lp__ 8.221840e+01 2.035543e-01 6.701522e+00 6.829873e+01 7.789941e+01
X50. X75. X97.5. n_eff Rhat
alpha 1.490835e-01 1.820241e-01 2.486097e-01 3471.265 0.9993581
beta 3.876053e-02 4.126745e-02 4.605342e-02 3545.768 0.9993534
gamma 1.787418e-04 2.278655e-04 3.277194e-04 2949.207 0.9999680
sigma 1.164994e-02 1.265773e-02 1.509514e-02 3734.709 0.9993841
lp__ 8.247441e+01 8.693106e+01 9.449232e+01 1083.893 1.0003436Reconstruction 1
ionRec <- read_excel(here("data", "Test 2.xlsx"), sheet = 2)
colnames(ionRec)[2:5] <- c("D47", "D47error", "Ion", "Ionerror")
ionRec <- na.omit(ionRec)
PredsBay <- rec.ion.bayesian(calModel = ionmodel[[1]],
recData = ionRec,
iter = 1000,
postcalsamples = 100, MC = FALSE)Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX13.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
In file included from <built-in>:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
#include <cmath>
^~~~~~~
1 error generated.
make: *** [foo.o] Error 1
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.001224 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 12.24 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 1000 [ 0%] (Warmup)
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Chain 1:
Chain 1: Elapsed Time: 14.124 seconds (Warm-up)
Chain 1: 10.97 seconds (Sampling)
Chain 1: 25.094 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000528 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 5.28 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: Iteration: 1 / 1000 [ 0%] (Warmup)
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Chain 2: Iteration: 1000 / 1000 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 13.702 seconds (Warm-up)
Chain 2: 11.488 seconds (Sampling)
Chain 2: 25.19 seconds (Total)
Chain 2: DT::datatable(
PredsBay,
extensions = c('Buttons', 'Scroller'),
options = list(
dom = 'Bfrtip',
buttons = list(
list(
extend = 'collection',
buttons = c('csv', 'excel', 'pdf'),
text = 'Download'
)
)
)
)Reconstruction 2
ionRec <- read_excel(here("data", "Test 2.xlsx"), sheet = 3)
colnames(ionRec)[2:5] <- c("D47", "D47error", "Ion", "Ionerror")
ionRec <- na.omit(ionRec)
PredsBay <- rec.ion.bayesian(calModel = ionmodel[[1]],
recData = ionRec,
iter = 1000,
postcalsamples = 100, MC = FALSE)Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX13.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
In file included from <built-in>:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
#include <cmath>
^~~~~~~
1 error generated.
make: *** [foo.o] Error 1
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000705 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 7.05 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 1000 [ 0%] (Warmup)
Chain 1: Iteration: 100 / 1000 [ 10%] (Warmup)
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Chain 1: Iteration: 1000 / 1000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 10.961 seconds (Warm-up)
Chain 1: 7.792 seconds (Sampling)
Chain 1: 18.753 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000357 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 3.57 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: Iteration: 1 / 1000 [ 0%] (Warmup)
Chain 2: Iteration: 100 / 1000 [ 10%] (Warmup)
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Chain 2: Iteration: 900 / 1000 [ 90%] (Sampling)
Chain 2: Iteration: 1000 / 1000 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 12.455 seconds (Warm-up)
Chain 2: 8.914 seconds (Sampling)
Chain 2: 21.369 seconds (Total)
Chain 2: DT::datatable(
PredsBay,
extensions = c('Buttons', 'Scroller'),
options = list(
dom = 'Bfrtip',
buttons = list(
list(
extend = 'collection',
buttons = c('csv', 'excel', 'pdf'),
text = 'Download'
)
)
)
)Test 3
Calibration
Table1 <- read_excel(here("data", "Test 3.xlsx"))
Table1$Material <- rep(1, nrow(Table1))
colnames(Table1)[c(5, 6, 2, 3, 8)] <- c("D47", "D47error", "Temperature", "TempError", "Ion")
# Check basic regression model
lm(Table1$D47 ~ Table1$Temperature)
Call:
lm(formula = Table1$D47 ~ Table1$Temperature)
Coefficients:
(Intercept) Table1$Temperature
0.18944 0.03624 # Fit Bayesian regression
ionmodel <- cal.ion.bayesian(calibrationData = Table1,
IonError = Table1$`Ion error`[1])Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX13.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
In file included from <built-in>:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
#include <cmath>
^~~~~~~
1 error generated.
make: *** [foo.o] Error 1
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 1).
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 8e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.8 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 1:
Chain 1: Gradient evaluation took 0.000111 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.11 seconds.
Chain 1Chain 2: Iteration: 1 / 2500 [ 0%] (Warmup)
: Adjust your expectations accordingly!
Chain 1:
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Chain 1:
Chain 1: Elapsed Time: 3.38 seconds (Warm-up)
Chain 1: 2.44 seconds (Sampling)
Chain 1: 5.82 seconds (Total)
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Chain 2: Iteration: 1750 / 2500 [ 70%] (Sampling)
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Chain 2: Iteration: 2500 / 2500 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 3.501 seconds (Warm-up)
Chain 2: 4.638 seconds (Sampling)
Chain 2: 8.139 seconds (Total)
Chain 2: parameters <- data.frame(rstan::summary(ionmodel[[1]])$summary)
DT::datatable(
parameters,
extensions = c('Buttons', 'Scroller'),
options = list(
dom = 'Bfrtip',
buttons = list(
list(
extend = 'collection',
buttons = c('csv', 'excel', 'pdf'),
text = 'Download'
)
)
)
)Reconstruction 1
ionRec <- read_excel(here("data", "Test 3.xlsx"), sheet = 2)
colnames(ionRec)[2:5] <- c("D47", "D47error", "Ion", "Ionerror")
ionRec <- na.omit(ionRec)
PredsBay <- rec.ion.bayesian(calModel = ionmodel[[1]],
recData = ionRec,
iter = 1000,
postcalsamples = 100, MC = FALSE)Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX13.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
In file included from <built-in>:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
#include <cmath>
^~~~~~~
1 error generated.
make: *** [foo.o] Error 1
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.001051 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 10.51 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 1000 [ 0%] (Warmup)
Chain 1: Iteration: 100 / 1000 [ 10%] (Warmup)
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Chain 1: Iteration: 900 / 1000 [ 90%] (Sampling)
Chain 1: Iteration: 1000 / 1000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 15.128 seconds (Warm-up)
Chain 1: 12.85 seconds (Sampling)
Chain 1: 27.978 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000538 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 5.38 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: Iteration: 1 / 1000 [ 0%] (Warmup)
Chain 2: Iteration: 100 / 1000 [ 10%] (Warmup)
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Chain 2: Iteration: 1000 / 1000 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 15.35 seconds (Warm-up)
Chain 2: 11.632 seconds (Sampling)
Chain 2: 26.982 seconds (Total)
Chain 2: DT::datatable(
PredsBay,
extensions = c('Buttons', 'Scroller'),
options = list(
dom = 'Bfrtip',
buttons = list(
list(
extend = 'collection',
buttons = c('csv', 'excel', 'pdf'),
text = 'Download'
)
)
)
)Reconstruction 2
ionRec <- read_excel(here("data", "Test 3.xlsx"), sheet = 3)
colnames(ionRec)[2:5] <- c("D47", "D47error", "Ion", "Ionerror")
ionRec <- na.omit(ionRec)
PredsBay <- rec.ion.bayesian(calModel = ionmodel[[1]],
recData = ionRec,
iter = 1000,
postcalsamples = 100, MC = FALSE)Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX13.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
In file included from <built-in>:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
#include <cmath>
^~~~~~~
1 error generated.
make: *** [foo.o] Error 1
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.00065 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 6.5 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 1000 [ 0%] (Warmup)
Chain 1: Iteration: 100 / 1000 [ 10%] (Warmup)
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Chain 1:
Chain 1: Elapsed Time: 14.434 seconds (Warm-up)
Chain 1: 8.137 seconds (Sampling)
Chain 1: 22.571 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000342 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 3.42 seconds.
Chain 2: Adjust your expectations accordingly!
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Chain 2:
Chain 2: Elapsed Time: 14.58 seconds (Warm-up)
Chain 2: 8.686 seconds (Sampling)
Chain 2: 23.266 seconds (Total)
Chain 2: DT::datatable(
PredsBay,
extensions = c('Buttons', 'Scroller'),
options = list(
dom = 'Bfrtip',
buttons = list(
list(
extend = 'collection',
buttons = c('csv', 'excel', 'pdf'),
text = 'Download'
)
)
)
)Test 4
Calibration
Table1 <- read_excel(here("data", "Test 4.xlsx"))
Table1$Material <- rep(1, nrow(Table1))
colnames(Table1)[c(5, 6, 2, 3, 8)] <- c("D47", "D47error", "Temperature", "TempError", "Ion")
# Check basic regression model
lm(Table1$D47 ~ Table1$Temperature)
Call:
lm(formula = Table1$D47 ~ Table1$Temperature)
Coefficients:
(Intercept) Table1$Temperature
0.24681 0.03173 # Fit Bayesian regression
ionmodel <- cal.ion.bayesian(calibrationData = Table1,
IonError = Table1$`Ion error`[1])Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX13.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
In file included from <built-in>:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
#include <cmath>
^~~~~~~
1 error generated.
make: *** [foo.o] Error 1
SAMPLING FOR MODEL 'anon_model
' NOW (CHAIN SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 21).
).
Chain 1:
Chain 1: Gradient evaluation took 7.4e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.74 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 2:
Chain 2: Gradient evaluation took 7.2e-05 seconds
Chain 2: Chain 1: Iteration: 1 / 2500 [ 0%] (Warmup)
1000 transitions using 10 leapfrog steps per transition would take 0.72 seconds.
Chain 2: Adjust your expectations accordingly!
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Chain 1:
Chain 1: Elapsed Time: 2.86 seconds (Warm-up)
Chain 1: 2.37 seconds (Sampling)
Chain 1: 5.23 seconds (Total)
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Chain 2: Iteration: 2500 / 2500 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 3.078 seconds (Warm-up)
Chain 2: 2.327 seconds (Sampling)
Chain 2: 5.405 seconds (Total)
Chain 2: parameters <- data.frame(rstan::summary(ionmodel[[1]])$summary)
DT::datatable(
parameters,
extensions = c('Buttons', 'Scroller'),
options = list(
dom = 'Bfrtip',
buttons = list(
list(
extend = 'collection',
buttons = c('csv', 'excel', 'pdf'),
text = 'Download'
)
)
)
)Reconstruction 1
ionRec <- read_excel(here("data", "Test 4.xlsx"), sheet = 2)
colnames(ionRec)[2:5] <- c("D47", "D47error", "Ion", "Ionerror")
ionRec <- na.omit(ionRec)
PredsBay <- rec.ion.bayesian(calModel = ionmodel[[1]],
recData = ionRec,
iter = 1000,
postcalsamples = 100, MC = FALSE)Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX13.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
In file included from <built-in>:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
#include <cmath>
^~~~~~~
1 error generated.
make: *** [foo.o] Error 1
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000935 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 9.35 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
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Chain 1:
Chain 1: Elapsed Time: 14.73 seconds (Warm-up)
Chain 1: 12.072 seconds (Sampling)
Chain 1: 26.802 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000497 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 4.97 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: Iteration: 1 / 1000 [ 0%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 13.855 seconds (Warm-up)
Chain 2: 11.747 seconds (Sampling)
Chain 2: 25.602 seconds (Total)
Chain 2: DT::datatable(
PredsBay,
extensions = c('Buttons', 'Scroller'),
options = list(
dom = 'Bfrtip',
buttons = list(
list(
extend = 'collection',
buttons = c('csv', 'excel', 'pdf'),
text = 'Download'
)
)
)
)Reconstruction 2
ionRec <- read_excel(here("data", "Test 4.xlsx"), sheet = 3)
colnames(ionRec)[2:5] <- c("D47", "D47error", "Ion", "Ionerror")
ionRec <- na.omit(ionRec)
PredsBay <- rec.ion.bayesian(calModel = ionmodel[[1]],
recData = ionRec,
iter = 1000,
postcalsamples = 100, MC = FALSE)Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX13.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
In file included from <built-in>:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
#include <cmath>
^~~~~~~
1 error generated.
make: *** [foo.o] Error 1
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000883 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 8.83 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 1000 [ 0%] (Warmup)
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Chain 1:
Chain 1: Elapsed Time: 13.51 seconds (Warm-up)
Chain 1: 8.544 seconds (Sampling)
Chain 1: 22.054 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000343 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 3.43 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: Iteration: 1 / 1000 [ 0%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 13.262 seconds (Warm-up)
Chain 2: 8.206 seconds (Sampling)
Chain 2: 21.468 seconds (Total)
Chain 2: DT::datatable(
PredsBay,
extensions = c('Buttons', 'Scroller'),
options = list(
dom = 'Bfrtip',
buttons = list(
list(
extend = 'collection',
buttons = c('csv', 'excel', 'pdf'),
text = 'Download'
)
)
)
)